1YRV

Novel Ubiquitin-Conjugating Enzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

A human ubiquitin conjugating enzyme (E2)-HECT E3 ligase structure-function screen.

Sheng, Y.Hong, J.H.Doherty, R.Srikumar, T.Shloush, J.Avvakumov, G.V.Walker, J.R.Xue, S.Neculai, D.Wan, J.W.Kim, S.K.Arrowsmith, C.H.Raught, B.Dhe-Paganon, S.

(2012) Mol Cell Proteomics 11: 329-341

  • DOI: 10.1074/mcp.O111.013706
  • Primary Citation of Related Structures:  
    3BZH, 3CEG, 2Z5D, 1Y6L, 2QGX, 1YH2, 1ZDN, 2OB4, 1YRV, 1ZUO

  • PubMed Abstract: 
  • Here we describe a systematic structure-function analysis of the human ubiquitin (Ub) E2 conjugating proteins, consisting of the determination of 15 new high-resolution three-dimensional structures of E2 catalytic domains, and autoubiquitylation assa ...

    Here we describe a systematic structure-function analysis of the human ubiquitin (Ub) E2 conjugating proteins, consisting of the determination of 15 new high-resolution three-dimensional structures of E2 catalytic domains, and autoubiquitylation assays for 26 Ub-loading E2s screened against a panel of nine different HECT (homologous to E6-AP carboxyl terminus) E3 ligase domains. Integration of our structural and biochemical data revealed several E2 surface properties associated with Ub chain building activity; (1) net positive or neutral E2 charge, (2) an "acidic trough" located near the catalytic Cys, surrounded by an extensive basic region, and (3) similarity to the previously described HECT binding signature in UBE2L3 (UbcH7). Mass spectrometry was used to characterize the autoubiquitylation products of a number of functional E2-HECT pairs, and demonstrated that HECT domains from different subfamilies catalyze the formation of very different types of Ub chains, largely independent of the E2 in the reaction. Our data set represents the first comprehensive analysis of E2-HECT E3 interactions, and thus provides a framework for better understanding the molecular mechanisms of ubiquitylation.


    Organizational Affiliation

    Department of Biology, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ubiquitin-conjugating ligase MGC351130A169Homo sapiensMutation(s): 0 
Gene Names: MGC35130UBE2U
EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt)
Find proteins for Q5VVX9 (Homo sapiens)
Explore Q5VVX9 
Go to UniProtKB:  Q5VVX9
NIH Common Fund Data Resources
PHAROS  Q5VVX9
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.244 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.968α = 90
b = 74.009β = 90
c = 119.733γ = 90
Software Package:
Software NamePurpose
CNSrefinement
d*TREKdata reduction
AMoREphasing
REFMACrefinement
d*TREKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-03-22
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-11-28
    Changes: Database references
  • Version 1.4: 2019-07-24
    Changes: Data collection, Refinement description